Hi friedns What will be the difference in the result of trimming with trimmomatic and prinseq? if we have 4 sequences of these features:
In the first sequence the for ASCII = 6 the quality score is 21. Also, after trimming we will have a sequence of length < 60 that is shorter than 60 bp length filter. The second sequence: In both ends it has ASCII of 6 with quality score of 21. Therefore, it needs trimming at both ends. After trimming we will have a sequence of length = 75 that is greater than 60 that is longer than the min length after trimming. Part3. Before trimming, sequence 3 has length = 55 that is shorter than the min length of 60. Part4. Sequence 4 has adapter contamination at the 3’ end. Also, it has length > 60 that is linger than minimum length =60.
prinseq is old and slow, I'd stick to Trimmomatic or fastp these days.